This　study　focused　on　the　differential　metabolomic　effects　between　water　extracts　of　Polygoni　Multiflori　Radix　and　Polygoni　Multiflori　Radix　Preparata　in　rats.　The　extracts　were　subsequently　administered　for　28　d.　Serum　biochemical　indicators　were　tested,　hematoxylin-eosin　staining　and　immunohistochemistry　staining　were　used　to　detect　histopathological　changes　in　the　livers.　Ultra-performance　LC/quadrupole　time-of-flight　mass　spectrometry　was　used　to　detect　the　changes　in　endogenous　metabolites.　Finally,　we　performed　detailed　analysis　of　the　changes　in　metabolic　pathways.　Hematoxylin-eosin　staining　and　immunohistochemistry　staining　results　indicated　that　the　water　extracts　of　Polygoni　Multiflori　Radix　and　Polygoni　Multiflori　Radix　Preparata　had　mild　liver　injury　effect.　Fifty-two　differential　endogenous　biomarkers　were　confirmed　as　potential　biomarkers　between　Polygoni　Multiflori　Radix　and　Polygoni　Multiflori　Radix　Preparata　groups.　In　the　positive　ion　mode,　the　biomarkers　included　31　Phosphatidyl　cholines　(PCs),　six　lysoPCs,　and　ceramide.　In　the　negative　ion　mode,　12　biomarkers　were　confirmed,　including　glycodeoxycholic　acid,　chenodeoxycholic　acid,　and　deoxycholic　acid,　etc.　In　Hydrophilic　Interaction　Liquid　Chromatography　(HILIC)　mode,　nine　biomarkers　were　confirmed,　including　niacinamide,　L-palmitoylcarnitine,　and　butyrylcarnitine,　etc.　Using　MetaboAnalyst　4.0,　six　related　metabolic　pathways,　including　taurine　and　hypotaurine　metabolism,　sphingolipid　metabolism,　glycerophospholipid　metabolism,　nicotinate　and　nicotinamide　metabolism,　arginine　and　proline　metabolism,　and　tryptophan　metabolism　and　primary　bile　synthesis,　were　confirmed　as　the　most　differential　pathways　between　the　Polygoni　Multiflori　Radix　and　Polygoni　Multiflori　Radix　Preparata　groups.